These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Anticlimax Boss: The Black Guardian has shades of this, with him being pretty easy despite easily killing Paul Luther, with attack that don't do that much damage and are easy to avoid. The problem though is that damaging in it's second phase borders on Guide Dang It.
Base Breaker: Shadow of the Eternals, especially its funding methods. Holy shit.
Part of it also has to do with the fact that the game's announcement came off the heels of a Kotaku article involving Silicon Knights' business practices, and much of the minds behind this game no longer work at the company (which went under a short time before the announcement of Shadow of the Eternals) or with Denis Dyack.
Breather Level: Michael Edwards's chapter, gameplay wise. You're given a bloody assault rifle to kill guardians with. Fitting, as it is the last chapter before the end.
Complete Monster: Pious. While he is The Dragon to an ancient evil god (you can choose from three), he is the main antagonist. When you first see him, he is a playable character, a Roman legionaire who stumbled on an ancient temple in Persia. In the end, he is corrupted by one of three artifacts and serves that god. It is not known when he crosses the Moral Event Horizon, but he is clearly over it for the rest of the game, committing horrific acts gleefully, including throwing hundreds of innocent people into a tower of corpses during Roberto Bianci's scenario (him included). He kills other characters you play as as well. It is also implied in one cutscene that he may intend to betray his god in the future (during the Xel'latoth arc) - take that much with a grain of salt, as Xel'lotath is completely out of her mind, but the rest still stands.
Crowning Music of Awesome: The soundtrack is notable for being very ambient and yet very memorable - especially when your character begins to lose sanity. The two bosses of the game also have awesome themes.
Arguably deconstructed with Shadow of the Eternals, which had an oft-repeated criticism that it was reaching far too high in its status as a follow-up to what was a very niche product, a fact which contributed to its failure in the crowdfunding arena.
Disappointing Last Level: Alex's chapter is largely a repeat of Edward's chapter, but with the gauntlet of guardian monsters replaced with a series of obnoxious electrified floors, making you stop every thirty seconds to replenish your shield.
The Mantorok rune. Even beyond the fact that Mantorok's Enchant Item spell is not only strong against all other ancients, it also poisons enemies you hit with it, doing additional damage. Its Recovery spell, likewise, recovers both health and sanity. A Mantorok shield will protect from all damage types and poison. A Mantorok Magick Pool spell will regenerate your health, magick and sanity all at the same time, making you nearly invincible. The most powerful spell in the entire game, in fact, is that the Reveal Invisible spell, normally cast only when the plot demands, will, if cast with a Mantorok rune, actually invert, making you invisible. This means that only boss monsters and Trappers will detect you. You can run around cutting their heads off and most monsters won't even fight back. Zombies will stand in one place swinging wildly and Gatekeepers will slowly rotate to face you, but will not attack.
It is possible to discover Magick Pool as early as Lindsey's chapter, although you don't get the scroll until Edward's. A Ulyaoth pool will render most Squishy Wizard characters nigh-invincible; a Mantorok one will render anyone invincible if they can afford the high magick cost.
If you so choose, you can walk around in circles to build up your magick, which you can use to heal and restore sanity.
Melee weapons are stupidly overpowered compared to the crossbow and various handguns; it's not until you find shotguns or rifles that distance attacking is superior to getting up close and personal.
"Pargon!" Explanation The "power" rune, added to increase spells' power level. Since all runes besides the two for the spell and the Ancient's rune will be this at higher levels, a 7 point spell might sound like "Tier, Pargon, Pargon, Santak, Pargon, Pargon, Ulyaoth!", so you will hear Pargon quite often
Nightmare Retardant: Michael Edwards' chapter is considerably less scary than any other part of the game. The unfathomable creatures of the beyond aren't quite as nightmarish when you're a heavy set firefighter with an assault rifle/grenade launcher.
Stop Helping Me!: Given all the numerous times a visual depiction of each Ancient's dominance over each other is shown, you will never find yourself forgetting how the Elemental Rock-Paper-Scissors works. You also need to sit through all the tutorials regardless of whether or not you've finished the game.
Ellia just wanted an adventure. She got it, probably saving Mantorok in the process. Pity it involved her imprisoned within her own dead body for centuries before the end.
Anthony, who fought against all odds, was cursed, knew he was likely a dead man, and ultimately failed. The fact he spent 600 years suffering before Paul released him from his torment doesn't make it better for him.
Paul Luther, who spends the duration of his story completely out of his depth and terrified out of his wits. Ultimately, his fate at the hands of the Guardian and the look on his face can't help but make you feel for the man.
Likewise, the custodian in Paul's chapter, his only ally who also ends up getting killed, possibly by Paul's own hand (ambiguous on purpose), and ends up having his soul bound to an altar until the defeat of Pious.
Karim ends up falling for a woman who sends him on an impossible quest to gain her affection. When he actually manages to reach his goal he discovers she's slept with the first rich charmer who came along, and is now dead because of it. Despite this, he still loves her and agrees to stay and guard the artifact sacrificing his own life. When Robert finally releases Karim from his duty it's clear the only thing he believes was gained from his sacrifice was aiding humanity.
Really, most of the characters, due to the fact that most of them are thrown into an age-old power struggle, with no preparation and an incredibly high chance of death or worse.